will-moore’s gists

will-moore / createImageFromTiffs.py

Last active March 18, 2019 15:35

createImageFromTiffs


	# See https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8679
	# and https://www.openmicroscopy.org/community/posting.php?mode=reply&f=6&t=8706

	import omero
	from omero.gateway import BlitzGateway
	from PIL import Image
	import numpy

	conn = BlitzGateway("username", "password", host="localhost", port=4064)

will-moore / renderingDefReset.py

Last active April 24, 2019 12:26

Reset rendering defs in OMERO, and regenerate thumbnails.


	import omero
	from omero.gateway import BlitzGateway

	# See https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8728

	conn = BlitzGateway("username", "password", host="localhost", port=4064)
	conn.connect()

	# Supports "Project", "Dataset" or "Image"

will-moore / idr_search_by_map_anns.py

Created May 8, 2019 12:30


	import omero
	from omero.gateway import BlitzGateway

	# See https://www.openmicroscopy.org/community/posting.php?mode=reply&f=6&t=8736

	idr_client = omero.client(host="idr.openmicroscopy.org", port=4064)
	idr_client.createSession('public', 'public')
	conn = BlitzGateway(client_obj=idr_client)

will-moore / simple_FRAP.py

Created June 11, 2019 08:23

OMERO training script


	# coding: utf-8

	# ### Please use the following link to try out the OMERO Python language bindings
	# https://docs.openmicroscopy.org/latest/omero/developers/Python.html

	# ### Import Packages required to connect to OMERO

	# In[1]:

will-moore / pixel_size_test.py

Last active January 23, 2020 14:29

For testing images with different pixel sizes

	from omero.model.enums import UnitsLength
	import omero
	from omero.rtypes import rstring

	from omero.gateway import BlitzGateway
	conn = BlitzGateway('user', 'password', port=4064, host='localhost')
	conn.connect()

	units = [
	UnitsLength.PICOMETER,

will-moore / nucleome_browser_chr.py

Created January 31, 2020 14:06


	import re
	from omero.gateway import BlitzGateway, MapAnnotationWrapper, LongAnnotationWrapper

	conn = BlitzGateway("user", "pass", port=4064, host="localhost")
	conn.connect()

	# Some example chromosome regions we want to annotate Images with...
	regions = [
	"hg19:chr19:15200000-15560000",

will-moore / add_ellipse_per_channel.py

Created February 10, 2020 15:03

Finds the brightest point in a plane and draws an ellipse around it. Useful for generating test ROIs.

	import omero
	from omero.rtypes import rdouble, rint
	import omero.grid
	from omero.gateway import BlitzGateway
	import numpy as np

	USERNAME = "user"
	PASSWORD = "password"
	HOST = "merge-ci-devspace.openmicroscopy.org"
	PORT = 4064

will-moore / FRAP_segmentation.py

Created February 25, 2020 22:07

Draw a Polygon around FRAP bleach spot. Works with FRAP images from https://downloads.openmicroscopy.org/images/DV/will/FRAP/


	import omero
	from omero.gateway import BlitzGateway
	from omero.rtypes import rint, rstring

	from skimage import morphology
	from skimage import measure

	conn = BlitzGateway('user', 'password', port=4064, host='localhost')
	conn.connect()

will-moore / nuclei_svs_segmentation.py

Created February 25, 2020 22:13

Adds Polygons around nuclei, works with image https://downloads.openmicroscopy.org/images/SVS/77928.svs Takes around 2 hours to run on that image, creating 160k polygons


	import omero
	from omero.gateway import BlitzGateway
	from omero.rtypes import rint, rstring

	from skimage import morphology
	from skimage import measure

	# Adapted from https://gist.github.com/stefanv/7c296c26b0c3624746f4317bed6a3540

will-moore / skimage_segmentation_dataset.py

Created March 18, 2020 14:13

Used on 8-bit images from idr0002 to segment to OMERO Polygons.


	import omero
	from omero.gateway import BlitzGateway
	from omero.rtypes import rint, rstring

	from skimage import morphology
	from skimage import measure

	# Adapted from https://gist.github.com/stefanv/7c296c26b0c3624746f4317bed6a3540

Will Moore will-moore